# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 02:42:59 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-(beta-D-glucopyranosyl)-6-propylfuro[2,3-d]pyrimidin-2(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC1=CC2=CN([C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)C(=O)N=C2O1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 D1K  D1K  3-(beta-D-glucopyranosyl)-6-propylfuro[2,3-d]pyrimidin-2(3H)-one  ligand  44  24  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D1K
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 D1K  N1    N  NR6   0  -0.563  -0.0717  -0.1906  -0.0923
 D1K  C2    C  CR6   0   0.610   0.3129  -0.0927   1.2688
 D1K  O2    O  O     0  -0.487  -0.5352  -0.0096   2.1372
 D1K  N3    N  N     0  -0.494   1.6451  -0.0968   1.5513
 D1K  C4    C  CR56  0   0.515   2.4614  -0.1939   0.5578
 D1K  C5    C  CR56  0  -0.079   2.1495  -0.2965  -0.8155
 D1K  O5    O  O     0  -0.448   3.7853  -0.2096   0.7172
 D1K  C6    C  CR16  0   0.041   0.8236  -0.2921  -1.1025
 D1K  C7    C  CR15  0  -0.442   3.4122  -0.3736  -1.5004
 D1K  C8    C  CR5   0   0.409   4.3549  -0.3180  -0.5440
 D1K  C9    C  CH2   0  -0.533   5.8331  -0.3253  -0.5933
 D1K  C1'   C  CH1   0   0.217  -1.4877  -0.2140  -0.4424
 D1K  C10   C  CH2   0  -0.427   6.4680   0.9840  -0.1129
 D1K  C11   C  CH3   0  -0.667   7.9859   0.9342  -0.2018
 D1K  C2'   C  CH1   0  -0.006  -2.2195  -1.4378   0.1063
 D1K  O2'   O  OH1   0  -0.666  -1.5865  -2.5618  -0.4470
 D1K  C3'   C  CH1   0  -0.033  -3.6827  -1.3287  -0.3089
 D1K  O3'   O  OH1   0  -0.676  -4.4120  -2.3879   0.2760
 D1K  C4'   C  CH1   0   0.036  -4.2579   0.0142   0.1358
 D1K  O4'   O  OH1   0  -0.672  -5.5780   0.1803  -0.3154
 D1K  C5'   C  CH1   0  -0.024  -3.4050   1.1402  -0.4502
 D1K  O5'   O  O2    0  -0.477  -2.0616   0.9824  -0.0295
 D1K  C6'   C  CH2   0  -0.158  -3.8638   2.5092   0.0015
 D1K  O6'   O  OH1   0  -0.670  -3.0848   3.4832  -0.6503
 D1K  H6    H  HCR6  0   0.332   0.4291  -0.3584  -2.1069
 D1K  H7    H  HCR5  0   0.276   3.5880  -0.4546  -2.5605
 D1K  H9    H  HCH2  0   0.258   6.2171  -1.1574   0.0065
 D1K  H9A   H  HCH2  0   0.261   6.1276  -0.5239  -1.6258
 D1K  H1'   H  HCH1  0   0.254  -1.5185  -0.2876  -1.5395
 D1K  H10   H  HCH2  0   0.231   6.0850   1.8115  -0.7149
 D1K  H10A  H  HCH2  0   0.231   6.1692   1.1834   0.9184
 D1K  H11   H  HCH3  0   0.223   8.3897   0.1289   0.4142
 D1K  H11A  H  HCH3  0   0.222   8.3183   0.7648  -1.2275
 D1K  H11B  H  HCH3  0   0.235   8.4310   1.8686   0.1401
 D1K  H2'   H  HCH1  0   0.248  -2.1692  -1.4454   1.1996
 D1K  HO2'  H  HOH1  0   0.458  -1.9886  -3.3498  -0.0678
 D1K  H3'   H  HCH1  0   0.232  -3.7428  -1.3798  -1.4056
 D1K  HO3'  H  HOH1  0   0.465  -4.8519  -2.8877  -0.4160
 D1K  H4'   H  HCH1  0   0.216  -4.2033   0.0769   1.2344
 D1K  HO4'  H  HOH1  0   0.453  -6.1104  -0.5309   0.0566
 D1K  H5'   H  HCH1  0   0.228  -3.4624   1.0882  -1.5503
 D1K  H6'   H  HCH2  0   0.216  -4.9267   2.6108  -0.2398
 D1K  H6'A  H  HCH2  0   0.200  -3.7713   2.5730   1.0944
 D1K  HO6'  H  HOH1  0   0.458  -3.4198   4.3483  -0.3994

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 D1K  N1   C2    single  1.418  0.020  1.418
 D1K  N1   C6    single  1.354  0.020  1.354
 D1K  N1   C1'   single  1.459  0.020  1.459
 D1K  C2   O2    double  1.217  0.020  1.217
 D1K  C2   N3    single  1.362  0.020  1.362
 D1K  N3   C4    double  1.290  0.020  1.290
 D1K  C4   C5    single  1.412  0.020  1.412
 D1K  C4   O5    single  1.334  0.020  1.334
 D1K  C5   C6    double  1.357  0.020  1.357
 D1K  C5   C7    single  1.439  0.020  1.439
 D1K  O5   C8    single  1.388  0.020  1.388
 D1K  C7   C8    double  1.344  0.020  1.344
 D1K  C8   C9    single  1.479  0.020  1.479
 D1K  C9   C10   single  1.532  0.020  1.532
 D1K  C1'  C2'   single  1.528  0.020  1.528
 D1K  C1'  O5'   single  1.390  0.020  1.390
 D1K  C10  C11   single  1.521  0.020  1.521
 D1K  C2'  O2'   single  1.404  0.020  1.404
 D1K  C2'  C3'   single  1.525  0.020  1.525
 D1K  C3'  O3'   single  1.413  0.020  1.413
 D1K  C3'  C4'   single  1.527  0.020  1.527
 D1K  C4'  O4'   single  1.405  0.020  1.405
 D1K  C4'  C5'   single  1.529  0.020  1.529
 D1K  C5'  O5'   single  1.417  0.020  1.417
 D1K  C5'  C6'   single  1.513  0.020  1.513
 D1K  C6'  O6'   single  1.407  0.020  1.407
 D1K  C6   H6    single  0.930  0.020  1.080
 D1K  C7   H7    single  0.930  0.020  1.080
 D1K  C9   H9    single  0.970  0.020  1.090
 D1K  C9   H9A   single  0.970  0.020  1.090
 D1K  C1'  H1'   single  0.970  0.020  1.090
 D1K  C10  H10   single  0.970  0.020  1.090
 D1K  C10  H10A  single  0.970  0.020  1.090
 D1K  C11  H11   single  0.970  0.020  1.090
 D1K  C11  H11A  single  0.970  0.020  1.090
 D1K  C11  H11B  single  0.970  0.020  1.090
 D1K  C2'  H2'   single  0.970  0.020  1.090
 D1K  O2'  HO2'  single  0.850  0.020  0.980
 D1K  C3'  H3'   single  0.970  0.020  1.090
 D1K  O3'  HO3'  single  0.850  0.020  0.980
 D1K  C4'  H4'   single  0.970  0.020  1.090
 D1K  O4'  HO4'  single  0.850  0.020  0.980
 D1K  C5'  H5'   single  0.970  0.020  1.090
 D1K  C6'  H6'   single  0.970  0.020  1.090
 D1K  C6'  H6'A  single  0.970  0.020  1.090
 D1K  O6'  HO6'  single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 D1K  C1'   N1   C6    117.50  3.000
 D1K  C1'   N1   C2    119.66  3.000
 D1K  C6    N1   C2    122.83  3.000
 D1K  N3    C2   O2    122.28  3.000
 D1K  N3    C2   N1    117.67  3.000
 D1K  O2    C2   N1    120.05  3.000
 D1K  C4    N3   C2    117.37  3.000
 D1K  O5    C4   C5    109.55  3.000
 D1K  O5    C4   N3    122.49  3.000
 D1K  C5    C4   N3    127.95  3.000
 D1K  C7    C5   C6    139.23  3.000
 D1K  C7    C5   C4    105.85  3.000
 D1K  C6    C5   C4    114.92  3.000
 D1K  C8    O5   C4    107.44  3.000
 D1K  H6    C6   C5    123.57  3.000
 D1K  H6    C6   N1    117.16  3.000
 D1K  C5    C6   N1    119.27  3.000
 D1K  H7    C7   C8    126.07  3.000
 D1K  H7    C7   C5    127.99  3.000
 D1K  C8    C7   C5    105.94  3.000
 D1K  C9    C8   C7    132.61  3.000
 D1K  C9    C8   O5    116.16  3.000
 D1K  C7    C8   O5    111.22  3.000
 D1K  H9A   C9   H9    106.57  3.000
 D1K  H9A   C9   C10   109.89  3.000
 D1K  H9    C9   C10   109.40  3.000
 D1K  H9A   C9   C8    107.58  3.000
 D1K  H9    C9   C8    109.63  3.000
 D1K  C10   C9   C8    113.54  3.000
 D1K  H1'   C1'  O5'   110.02  3.000
 D1K  H1'   C1'  C2'   106.93  3.000
 D1K  O5'   C1'  C2'   112.65  3.000
 D1K  H1'   C1'  N1    105.53  3.000
 D1K  O5'   C1'  N1    108.41  3.000
 D1K  C2'   C1'  N1    113.05  3.000
 D1K  H10A  C10  H10   106.62  3.000
 D1K  H10A  C10  C11   109.52  3.000
 D1K  H10   C10  C11   110.02  3.000
 D1K  H10A  C10  C9    109.80  3.000
 D1K  H10   C10  C9    109.22  3.000
 D1K  C11   C10  C9    111.54  3.000
 D1K  H11B  C11  H11A  107.66  3.000
 D1K  H11B  C11  H11   107.72  3.000
 D1K  H11A  C11  H11   107.65  3.000
 D1K  H11B  C11  C10   111.17  3.000
 D1K  H11A  C11  C10   111.34  3.000
 D1K  H11   C11  C10   111.12  3.000
 D1K  H2'   C2'  C3'   108.46  3.000
 D1K  H2'   C2'  O2'   111.56  3.000
 D1K  C3'   C2'  O2'   112.50  3.000
 D1K  H2'   C2'  C1'   110.01  3.000
 D1K  C3'   C2'  C1'   107.73  3.000
 D1K  O2'   C2'  C1'   106.49  3.000
 D1K  HO2'  O2'  C2'   108.17  3.000
 D1K  H3'   C3'  C4'   108.10  3.000
 D1K  H3'   C3'  O3'   110.48  3.000
 D1K  C4'   C3'  O3'   110.14  3.000
 D1K  H3'   C3'  C2'   108.71  3.000
 D1K  C4'   C3'  C2'   110.18  3.000
 D1K  O3'   C3'  C2'   109.21  3.000
 D1K  HO3'  O3'  C3'   109.17  3.000
 D1K  H4'   C4'  C5'   108.22  3.000
 D1K  H4'   C4'  O4'   111.11  3.000
 D1K  C5'   C4'  O4'   108.29  3.000
 D1K  H4'   C4'  C3'   108.77  3.000
 D1K  C5'   C4'  C3'   109.02  3.000
 D1K  O4'   C4'  C3'   111.36  3.000
 D1K  HO4'  O4'  C4'   107.94  3.000
 D1K  H5'   C5'  C6'   108.95  3.000
 D1K  H5'   C5'  O5'   109.90  3.000
 D1K  C6'   C5'  O5'   107.44  3.000
 D1K  H5'   C5'  C4'   108.58  3.000
 D1K  C6'   C5'  C4'   112.50  3.000
 D1K  O5'   C5'  C4'   109.45  3.000
 D1K  C5'   O5'  C1'   113.54  3.000
 D1K  H6'A  C6'  H6'   107.19  3.000
 D1K  H6'A  C6'  O6'   111.96  3.000
 D1K  H6'   C6'  O6'   111.79  3.000
 D1K  H6'A  C6'  C5'   108.91  3.000
 D1K  H6'   C6'  C5'   108.22  3.000
 D1K  O6'   C6'  C5'   108.67  3.000
 D1K  HO6'  O6'  C6'   108.01  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 D1K  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 D1K  CONST_02  C6   N1   C2   N3     0.00   0.0  0
 D1K  CONST_03  C1'  N1   C2   N3   180.00   0.0  0
 D1K  CONST_04  C6   N1   C2   O2   180.00   0.0  0
 D1K  CONST_05  C1'  N1   C2   O2     0.00   0.0  0
 D1K  CONST_06  C4   N3   C2   O2   180.00   0.0  0
 D1K  Var_01    C10  C9   C8   O5   -64.24  30.0  3
 D1K  Var_02    C11  C10  C9   C8  -179.17  30.0  3
 D1K  Var_03    H11  C11  C10  C9   -60.10  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 D1K  chir_01  C1'  N1   C2'  O5'  negativ
 D1K  chir_02  C2'  O2'  C1'  C3'  negativ
 D1K  chir_03  C3'  O3'  C2'  C4'  positiv
 D1K  chir_04  C4'  O4'  C5'  C3'  positiv
 D1K  chir_05  C5'  O5'  C4'  C6'  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 D1K  plan-1  N1   0.020
 D1K  plan-1  C2   0.020
 D1K  plan-1  O2   0.020
 D1K  plan-1  N3   0.020
 D1K  plan-1  C4   0.020
 D1K  plan-1  C5   0.020
 D1K  plan-1  O5   0.020
 D1K  plan-1  C6   0.020
 D1K  plan-1  C7   0.020
 D1K  plan-1  C8   0.020
 D1K  plan-1  C9   0.020
 D1K  plan-1  C1'  0.020
 D1K  plan-1  H6   0.020
 D1K  plan-1  H7   0.020

